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        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
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        About MultiQC

        This report was generated using MultiQC, version 1.30

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        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        This report has been generated by the nf-core/rnaseq analysis pipeline. For information about how to interpret these results, please see the documentation.
        Report generated on 2025-09-04, 08:45 -03 based on data in: /mnt/beegfs/scratch/gmdazevedo/rstudio/sjogren_rnaseq/ERP129369/assets/work/ba/b4c4ead6d7cd4e05ba3ae7f0cc2c87

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        General Statistics

        Showing 123/123 rows and 26/46 columns.
        Sample Name% rRNAdupIntDuplication5'-3' biasM AlignedExonicIntronicIntergenicOverlapping ExonProper PairsError rateNon-primaryReads mapped% Mapped% Proper pairs% MapQ 0 readsTotal seqsMean insertReadsReads mapped% Reads mappedTotal readsAlignedAlignedUniq alignedUniq alignedMultimappedDupsGCAvg lenMedian lenFailedSeqs% Duplication% > Q30Mb Q30 basesReads After FilteringGC content% PF% AdapterDupsGCAvg lenMedian lenFailedSeqs
        ERR5974709
        0.0
        0.2
        55.5%
        1.21
        61.2M
        91.9M
        12.3M
        2.9M
        3.4M
        35.8%
        0.35%
        21.7M
        122.4M
        100.0%
        100.0%
        1.5%
        122.4M
        1001.4bp
        144.1M
        144.1M
        100.0%
        64.0M
        61.2M
        95.6%
        56.6M
        88.4%
        4.6M
        34.1%
        93.1%
        15721.7Mb
        128.1M
        50.4%
        98.9%
        1.7%
        ERR5974709_1
        69.7%
        50.0%
        133bp
        147bp
        27%
        64.8M
        70.0%
        50.0%
        132bp
        142bp
        27%
        64.0M
        ERR5974709_2
        67.3%
        50.0%
        133bp
        147bp
        18%
        64.8M
        68.0%
        50.0%
        132bp
        142bp
        18%
        64.0M
        ERR5974710
        0.0
        0.2
        44.3%
        1.22
        43.4M
        60.3M
        12.1M
        3.5M
        2.4M
        44.7%
        0.41%
        15.2M
        86.7M
        100.0%
        100.0%
        1.3%
        86.7M
        1109.7bp
        102.0M
        102.0M
        100.0%
        45.6M
        43.4M
        95.0%
        39.8M
        87.1%
        3.6M
        26.0%
        93.3%
        11096.8Mb
        91.3M
        51.7%
        98.9%
        1.7%
        ERR5974710_1
        61.6%
        51.0%
        131bp
        142bp
        27%
        46.2M
        61.9%
        51.0%
        130bp
        142bp
        27%
        45.6M
        ERR5974710_2
        60.0%
        51.0%
        131bp
        142bp
        27%
        46.2M
        60.6%
        51.0%
        130bp
        142bp
        27%
        45.6M
        ERR5974711
        0.0
        0.2
        52.4%
        1.19
        59.4M
        88.4M
        11.8M
        3.2M
        3.2M
        36.1%
        0.33%
        28.5M
        118.8M
        100.0%
        100.0%
        2.3%
        118.8M
        1037.1bp
        147.3M
        147.3M
        100.0%
        62.4M
        59.4M
        95.2%
        54.2M
        86.9%
        5.2M
        33.6%
        94.1%
        15163.1Mb
        124.8M
        51.8%
        99.1%
        1.5%
        ERR5974711_1
        68.1%
        51.0%
        130bp
        137bp
        27%
        63.0M
        68.3%
        51.0%
        129bp
        137bp
        27%
        62.4M
        ERR5974711_2
        67.5%
        51.0%
        130bp
        137bp
        27%
        63.0M
        68.0%
        51.0%
        129bp
        137bp
        27%
        62.4M
        ERR5974712
        0.0
        0.2
        48.3%
        1.20
        57.0M
        84.5M
        12.5M
        3.6M
        3.4M
        42.0%
        0.35%
        18.6M
        113.9M
        100.0%
        100.0%
        1.3%
        113.9M
        995.7bp
        132.6M
        132.6M
        100.0%
        59.7M
        57.0M
        95.4%
        52.9M
        88.5%
        4.1M
        27.6%
        93.5%
        13990.6Mb
        119.5M
        51.6%
        98.8%
        1.9%
        ERR5974712_1
        64.4%
        51.0%
        126bp
        137bp
        18%
        60.5M
        64.7%
        51.0%
        125bp
        132bp
        18%
        59.7M
        ERR5974712_2
        62.9%
        51.0%
        126bp
        137bp
        18%
        60.5M
        63.5%
        51.0%
        126bp
        132bp
        18%
        59.7M
        ERR5974713
        0.0
        0.1
        41.5%
        1.25
        43.7M
        63.7M
        10.7M
        3.0M
        2.5M
        48.3%
        0.33%
        13.0M
        87.4M
        100.0%
        100.0%
        1.1%
        87.4M
        968.7bp
        100.3M
        100.3M
        100.0%
        45.5M
        43.7M
        96.1%
        40.7M
        89.6%
        2.9M
        24.1%
        93.4%
        11213.8Mb
        90.9M
        51.2%
        98.8%
        1.7%
        ERR5974713_1
        60.0%
        51.0%
        133bp
        147bp
        18%
        46.0M
        60.3%
        51.0%
        132bp
        147bp
        18%
        45.5M
        ERR5974713_2
        58.6%
        51.0%
        133bp
        147bp
        18%
        46.0M
        59.1%
        51.0%
        132bp
        147bp
        18%
        45.5M
        ERR5974714
        0.0
        0.1
        44.6%
        1.23
        40.3M
        59.9M
        9.3M
        2.2M
        2.3M
        45.1%
        0.32%
        13.6M
        80.7M
        100.0%
        100.0%
        1.4%
        80.7M
        872.5bp
        94.3M
        94.3M
        100.0%
        42.0M
        40.3M
        96.0%
        37.6M
        89.5%
        2.7M
        27.1%
        93.2%
        10147.9Mb
        84.1M
        50.0%
        98.8%
        1.7%
        ERR5974714_1
        62.5%
        49.0%
        131bp
        142bp
        18%
        42.5M
        62.8%
        49.0%
        130bp
        142bp
        18%
        42.0M
        ERR5974714_2
        60.9%
        50.0%
        131bp
        142bp
        18%
        42.5M
        61.5%
        50.0%
        130bp
        142bp
        18%
        42.0M
        ERR5974715
        0.0
        0.2
        50.6%
        1.13
        58.4M
        87.2M
        11.5M
        2.9M
        3.3M
        37.1%
        0.40%
        29.2M
        116.8M
        100.0%
        100.0%
        2.5%
        116.8M
        1146.7bp
        146.1M
        146.1M
        100.0%
        61.3M
        58.4M
        95.3%
        53.3M
        86.9%
        5.2M
        30.8%
        93.5%
        15039.4Mb
        122.6M
        51.9%
        99.0%
        1.8%
        ERR5974715_1
        66.5%
        51.0%
        132bp
        147bp
        27%
        61.9M
        66.8%
        51.0%
        131bp
        142bp
        27%
        61.3M
        ERR5974715_2
        64.6%
        51.0%
        132bp
        147bp
        27%
        61.9M
        65.2%
        51.0%
        131bp
        142bp
        27%
        61.3M
        ERR5974716
        0.0
        0.2
        49.1%
        1.19
        47.8M
        72.3M
        9.3M
        2.5M
        2.7M
        40.8%
        0.32%
        17.5M
        95.6M
        100.0%
        100.0%
        1.6%
        95.6M
        992.5bp
        113.1M
        113.1M
        100.0%
        50.1M
        47.8M
        95.4%
        44.3M
        88.5%
        3.5M
        31.0%
        93.7%
        11956.7Mb
        100.1M
        51.1%
        99.0%
        1.7%
        ERR5974716_1
        65.1%
        51.0%
        128bp
        137bp
        18%
        50.6M
        65.3%
        51.0%
        128bp
        137bp
        18%
        50.1M
        ERR5974716_2
        63.9%
        51.0%
        128bp
        137bp
        18%
        50.6M
        64.4%
        51.0%
        128bp
        137bp
        18%
        50.1M
        ERR5974717
        0.0
        0.2
        54.0%
        1.17
        43.8M
        67.6M
        7.5M
        1.6M
        2.4M
        35.0%
        0.31%
        21.2M
        87.7M
        100.0%
        100.0%
        2.4%
        87.7M
        965.9bp
        108.9M
        108.9M
        100.0%
        45.8M
        43.8M
        95.7%
        40.3M
        88.0%
        3.5M
        34.0%
        93.1%
        10832.3Mb
        91.6M
        51.0%
        98.8%
        2.0%
        ERR5974717_1
        68.4%
        50.0%
        128bp
        142bp
        18%
        46.3M
        68.6%
        50.0%
        127bp
        137bp
        18%
        45.8M
        ERR5974717_2
        66.1%
        51.0%
        128bp
        142bp
        18%
        46.3M
        66.8%
        51.0%
        127bp
        137bp
        18%
        45.8M
        ERR5974718
        0.0
        0.1
        57.1%
        1.16
        50.3M
        78.8M
        7.8M
        1.5M
        2.5M
        32.9%
        0.32%
        24.1M
        100.6M
        100.0%
        100.0%
        2.4%
        100.6M
        996.4bp
        124.7M
        124.7M
        100.0%
        52.4M
        50.3M
        96.1%
        46.1M
        88.0%
        4.2M
        38.2%
        93.3%
        12710.0Mb
        104.7M
        50.7%
        99.1%
        2.1%
        ERR5974718_1
        71.6%
        50.0%
        131bp
        142bp
        18%
        52.9M
        71.9%
        50.0%
        130bp
        142bp
        18%
        52.4M
        ERR5974718_2
        69.7%
        50.0%
        131bp
        142bp
        18%
        52.9M
        70.3%
        50.0%
        130bp
        142bp
        18%
        52.4M
        ERR5974719
        0.0
        0.2
        51.4%
        1.17
        57.3M
        87.5M
        11.0M
        2.6M
        3.2M
        38.6%
        0.32%
        22.2M
        114.5M
        100.0%
        100.0%
        1.8%
        114.5M
        1010.4bp
        136.7M
        136.7M
        100.0%
        59.7M
        57.3M
        95.9%
        53.0M
        88.8%
        4.2M
        31.4%
        93.3%
        14503.5Mb
        119.4M
        51.2%
        99.0%
        1.7%
        ERR5974719_1
        66.6%
        51.0%
        131bp
        142bp
        18%
        60.3M
        66.8%
        51.0%
        130bp
        137bp
        18%
        59.7M
        ERR5974719_2
        64.5%
        51.0%
        131bp
        142bp
        18%
        60.3M
        65.1%
        51.0%
        130bp
        137bp
        18%
        59.7M
        ERR5974720
        0.0
        0.2
        53.3%
        1.19
        56.8M
        86.3M
        10.9M
        2.7M
        3.3M
        37.2%
        0.37%
        21.6M
        113.6M
        100.0%
        100.0%
        1.7%
        113.6M
        1023.5bp
        135.1M
        135.1M
        100.0%
        59.7M
        56.8M
        95.1%
        52.6M
        88.0%
        4.2M
        31.1%
        92.7%
        14526.1Mb
        119.4M
        51.0%
        98.8%
        1.8%
        ERR5974720_1
        68.1%
        50.0%
        132bp
        147bp
        18%
        60.4M
        68.4%
        50.0%
        131bp
        142bp
        18%
        59.7M
        ERR5974720_2
        64.9%
        51.0%
        132bp
        147bp
        18%
        60.4M
        65.6%
        50.0%
        131bp
        142bp
        18%
        59.7M
        ERR5974721
        0.0
        0.2
        54.4%
        1.15
        58.6M
        88.6M
        10.2M
        2.9M
        3.3M
        35.6%
        0.32%
        24.5M
        117.2M
        100.0%
        100.0%
        1.8%
        117.2M
        1055.1bp
        141.8M
        141.8M
        100.0%
        61.6M
        58.6M
        95.2%
        53.8M
        87.3%
        4.8M
        35.3%
        93.8%
        14366.4Mb
        123.1M
        51.1%
        99.0%
        1.8%
        ERR5974721_1
        69.7%
        51.0%
        125bp
        132bp
        27%
        62.2M
        69.9%
        51.0%
        125bp
        132bp
        27%
        61.6M
        ERR5974721_2
        68.6%
        51.0%
        125bp
        132bp
        27%
        62.2M
        69.2%
        51.0%
        125bp
        132bp
        27%
        61.6M
        ERR5974722
        0.0
        0.2
        45.2%
        1.18
        59.5M
        86.2M
        13.9M
        3.7M
        3.5M
        41.4%
        0.37%
        29.6M
        119.0M
        100.0%
        100.0%
        2.6%
        119.0M
        1066.1bp
        148.5M
        148.5M
        100.0%
        62.7M
        59.5M
        94.8%
        54.6M
        87.0%
        4.9M
        26.5%
        93.3%
        15181.7Mb
        125.5M
        52.3%
        98.7%
        1.8%
        ERR5974722_1
        62.5%
        52.0%
        130bp
        142bp
        27%
        63.5M
        62.7%
        52.0%
        130bp
        137bp
        27%
        62.7M
        ERR5974722_2
        60.3%
        52.0%
        130bp
        142bp
        27%
        63.5M
        60.9%
        52.0%
        130bp
        137bp
        27%
        62.7M
        ERR5974723
        0.0
        0.2
        51.6%
        1.23
        57.7M
        86.5M
        11.9M
        2.8M
        3.2M
        38.3%
        0.38%
        22.3M
        115.4M
        100.0%
        100.0%
        1.7%
        115.4M
        965.8bp
        137.7M
        137.7M
        100.0%
        60.6M
        57.7M
        95.2%
        53.4M
        88.0%
        4.4M
        31.8%
        93.5%
        14216.7Mb
        121.3M
        51.6%
        98.9%
        1.7%
        ERR5974723_1
        67.1%
        51.0%
        126bp
        137bp
        18%
        61.3M
        67.4%
        51.0%
        126bp
        132bp
        18%
        60.6M
        ERR5974723_2
        64.9%
        51.0%
        126bp
        137bp
        18%
        61.3M
        65.6%
        51.0%
        126bp
        132bp
        18%
        60.6M
        ERR5974724
        0.0
        1.1
        79.4%
        1.21
        58.7M
        87.4M
        11.0M
        2.2M
        3.1M
        14.3%
        0.31%
        39.2M
        117.4M
        100.0%
        100.0%
        3.9%
        117.4M
        941.3bp
        156.6M
        156.6M
        100.0%
        61.4M
        58.7M
        95.6%
        53.2M
        86.6%
        5.5M
        53.2%
        93.5%
        14844.8Mb
        122.8M
        49.8%
        98.9%
        1.8%
        ERR5974724_1
        79.3%
        49.0%
        130bp
        142bp
        27%
        62.1M
        79.6%
        49.0%
        129bp
        137bp
        27%
        61.4M
        ERR5974724_2
        77.9%
        49.0%
        130bp
        142bp
        27%
        62.1M
        78.6%
        49.0%
        129bp
        137bp
        27%
        61.4M
        ERR5974725
        0.0
        0.2
        47.1%
        1.13
        58.9M
        88.3M
        12.6M
        2.9M
        3.5M
        41.8%
        0.31%
        23.3M
        117.7M
        100.0%
        100.0%
        1.8%
        117.7M
        1016.2bp
        141.0M
        141.0M
        100.0%
        61.2M
        58.9M
        96.1%
        54.5M
        89.0%
        4.3M
        29.0%
        93.5%
        14652.7Mb
        122.4M
        51.7%
        99.0%
        1.6%
        ERR5974725_1
        63.6%
        51.0%
        129bp
        137bp
        18%
        61.8M
        63.9%
        51.0%
        128bp
        137bp
        18%
        61.2M
        ERR5974725_2
        61.7%
        51.0%
        129bp
        137bp
        18%
        61.8M
        62.3%
        51.0%
        128bp
        137bp
        18%
        61.2M
        ERR5974726
        0.0
        0.2
        40.7%
        1.17
        46.5M
        69.2M
        11.6M
        2.3M
        2.9M
        48.7%
        0.36%
        14.9M
        92.9M
        100.0%
        100.0%
        1.4%
        92.9M
        1024.6bp
        107.8M
        107.8M
        100.0%
        48.0M
        46.5M
        96.7%
        43.5M
        90.5%
        3.0M
        22.5%
        93.1%
        11556.3Mb
        96.1M
        50.8%
        99.0%
        1.7%
        ERR5974726_1
        57.0%
        50.0%
        130bp
        142bp
        18%
        48.5M
        57.2%
        50.0%
        129bp
        137bp
        18%
        48.0M
        ERR5974726_2
        54.7%
        50.0%
        130bp
        142bp
        18%
        48.5M
        55.2%
        50.0%
        129bp
        137bp
        18%
        48.0M
        ERR5974727
        0.0
        0.2
        43.4%
        1.16
        59.1M
        89.0M
        13.6M
        2.7M
        3.6M
        45.7%
        0.31%
        20.8M
        118.2M
        100.0%
        100.0%
        1.6%
        118.2M
        1110.0bp
        139.0M
        139.0M
        100.0%
        61.7M
        59.1M
        95.8%
        55.1M
        89.3%
        4.0M
        25.9%
        93.4%
        15028.0Mb
        123.4M
        51.7%
        98.9%
        1.8%
        ERR5974727_1
        60.9%
        51.0%
        131bp
        142bp
        18%
        62.4M
        61.1%
        51.0%
        131bp
        142bp
        18%
        61.7M
        ERR5974727_2
        58.7%
        51.0%
        131bp
        142bp
        18%
        62.4M
        59.2%
        51.0%
        131bp
        142bp
        18%
        61.7M
        ERR5974728
        0.0
        0.1
        42.2%
        1.14
        40.3M
        61.1M
        8.8M
        1.5M
        2.3M
        46.8%
        0.34%
        14.1M
        80.6M
        100.0%
        100.0%
        1.5%
        80.6M
        1030.5bp
        94.7M
        94.7M
        100.0%
        41.9M
        40.3M
        96.3%
        37.6M
        89.8%
        2.7M
        26.7%
        93.4%
        10063.2Mb
        83.7M
        50.9%
        99.0%
        1.7%
        ERR5974728_1
        59.8%
        50.0%
        130bp
        142bp
        18%
        42.3M
        60.0%
        50.0%
        129bp
        137bp
        18%
        41.9M
        ERR5974728_2
        58.0%
        50.0%
        130bp
        142bp
        18%
        42.3M
        58.5%
        50.0%
        129bp
        137bp
        18%
        41.9M
        ERR5974729
        0.0
        0.1
        52.2%
        1.12
        57.4M
        84.5M
        11.7M
        2.7M
        3.3M
        36.0%
        0.34%
        28.8M
        114.9M
        100.0%
        100.0%
        2.1%
        114.9M
        1160.1bp
        143.6M
        143.6M
        100.0%
        60.2M
        57.4M
        95.3%
        51.9M
        86.1%
        5.6M
        33.7%
        93.3%
        14747.2Mb
        120.5M
        51.0%
        98.9%
        1.9%
        ERR5974729_1
        68.1%
        50.0%
        132bp
        147bp
        27%
        60.9M
        68.4%
        50.0%
        131bp
        142bp
        27%
        60.2M
        ERR5974729_2
        66.2%
        51.0%
        132bp
        147bp
        27%
        60.9M
        66.8%
        50.0%
        131bp
        142bp
        27%
        60.2M
        ERR5974730
        0.0
        0.2
        51.6%
        1.16
        57.0M
        84.5M
        13.0M
        2.4M
        3.2M
        36.5%
        0.33%
        28.7M
        114.1M
        100.0%
        100.0%
        2.6%
        114.1M
        1029.6bp
        142.7M
        142.7M
        100.0%
        59.7M
        57.0M
        95.5%
        52.3M
        87.5%
        4.8M
        31.6%
        93.1%
        14485.1Mb
        119.5M
        50.7%
        98.9%
        1.8%
        ERR5974730_1
        65.5%
        50.0%
        131bp
        142bp
        18%
        60.4M
        65.8%
        50.0%
        130bp
        142bp
        18%
        59.7M
        ERR5974730_2
        63.1%
        50.0%
        131bp
        142bp
        18%
        60.4M
        63.7%
        50.0%
        130bp
        142bp
        18%
        59.7M
        ERR5974731
        0.0
        0.1
        47.3%
        1.15
        45.7M
        68.8M
        9.5M
        1.9M
        2.7M
        40.2%
        0.29%
        21.7M
        91.4M
        100.0%
        100.0%
        2.4%
        91.4M
        979.8bp
        113.1M
        113.1M
        100.0%
        47.5M
        45.7M
        96.2%
        42.1M
        88.6%
        3.6M
        30.2%
        93.5%
        11382.5Mb
        95.0M
        51.2%
        99.1%
        1.8%
        ERR5974731_1
        62.9%
        51.0%
        129bp
        137bp
        18%
        47.9M
        63.1%
        51.0%
        128bp
        137bp
        18%
        47.5M
        ERR5974731_2
        61.3%
        51.0%
        129bp
        137bp
        18%
        47.9M
        61.8%
        51.0%
        128bp
        137bp
        18%
        47.5M
        ERR5974732
        0.0
        0.2
        48.6%
        1.16
        62.9M
        90.4M
        16.0M
        3.6M
        3.8M
        39.6%
        0.36%
        28.5M
        125.9M
        100.0%
        100.0%
        2.2%
        125.9M
        1100.2bp
        154.4M
        154.4M
        100.0%
        66.3M
        62.9M
        95.0%
        57.7M
        87.1%
        5.2M
        29.5%
        93.4%
        16384.8Mb
        132.5M
        51.6%
        99.1%
        1.4%
        ERR5974732_1
        63.2%
        51.0%
        133bp
        147bp
        27%
        66.9M
        63.4%
        51.0%
        133bp
        142bp
        27%
        66.3M
        ERR5974732_2
        61.0%
        51.0%
        133bp
        147bp
        27%
        66.9M
        61.5%
        51.0%
        133bp
        142bp
        27%
        66.3M
        ERR5974733
        0.0
        0.2
        56.2%
        1.18
        59.7M
        88.9M
        12.4M
        2.4M
        3.6M
        33.6%
        0.31%
        27.7M
        119.3M
        100.0%
        100.0%
        2.2%
        119.3M
        1011.7bp
        147.1M
        147.1M
        100.0%
        62.2M
        59.7M
        96.0%
        54.7M
        88.0%
        5.0M
        36.1%
        93.3%
        15118.0Mb
        124.3M
        50.6%
        99.0%
        1.9%
        ERR5974733_1
        68.7%
        50.0%
        131bp
        142bp
        18%
        62.8M
        69.0%
        50.0%
        130bp
        137bp
        18%
        62.2M
        ERR5974733_2
        66.8%
        50.0%
        131bp
        142bp
        18%
        62.8M
        67.5%
        50.0%
        130bp
        137bp
        18%
        62.2M
        ERR5974734
        0.0
        0.1
        45.8%
        1.17
        46.2M
        69.7M
        9.3M
        1.9M
        2.6M
        41.9%
        0.34%
        20.7M
        92.5M
        100.0%
        100.0%
        2.0%
        92.5M
        1011.5bp
        113.2M
        113.2M
        100.0%
        48.3M
        46.2M
        95.7%
        42.5M
        87.8%
        3.8M
        28.5%
        93.6%
        11742.2Mb
        96.7M
        50.8%
        99.0%
        2.3%
        ERR5974734_1
        63.4%
        50.0%
        131bp
        142bp
        27%
        48.8M
        63.7%
        50.0%
        130bp
        142bp
        27%
        48.3M
        ERR5974734_2
        61.9%
        50.0%
        131bp
        142bp
        27%
        48.8M
        62.4%
        50.0%
        130bp
        142bp
        27%
        48.3M
        ERR5974735
        0.0
        0.1
        47.5%
        1.14
        56.8M
        83.9M
        12.9M
        2.8M
        3.4M
        40.0%
        0.33%
        26.7M
        113.6M
        100.0%
        100.0%
        2.2%
        113.6M
        1055.5bp
        140.3M
        140.3M
        100.0%
        59.6M
        56.8M
        95.3%
        52.0M
        87.2%
        4.8M
        29.4%
        93.6%
        14446.4Mb
        119.2M
        52.4%
        99.1%
        1.8%
        ERR5974735_1
        64.1%
        52.0%
        130bp
        142bp
        27%
        60.2M
        64.3%
        52.0%
        130bp
        137bp
        27%
        59.6M
        ERR5974735_2
        62.8%
        52.0%
        130bp
        142bp
        27%
        60.2M
        63.3%
        52.0%
        130bp
        137bp
        27%
        59.6M
        ERR5974736
        0.0
        0.2
        42.3%
        1.18
        63.9M
        94.7M
        15.5M
        3.2M
        3.9M
        47.0%
        0.31%
        21.1M
        127.8M
        100.0%
        100.0%
        1.4%
        127.8M
        974.4bp
        148.9M
        148.9M
        100.0%
        66.3M
        63.9M
        96.4%
        59.6M
        90.0%
        4.3M
        26.2%
        93.7%
        15838.8Mb
        132.5M
        51.6%
        99.1%
        1.6%
        ERR5974736_1
        60.6%
        51.0%
        128bp
        137bp
        18%
        66.9M
        60.9%
        51.0%
        128bp
        137bp
        18%
        66.3M
        ERR5974736_2
        59.3%
        51.0%
        128bp
        137bp
        18%
        66.9M
        59.8%
        51.0%
        128bp
        137bp
        18%
        66.3M
        ERR5974737
        0.0
        0.2
        47.9%
        1.20
        43.2M
        63.1M
        8.1M
        1.6M
        2.5M
        32.5%
        0.36%
        42.1M
        86.4M
        100.0%
        100.0%
        6.0%
        86.4M
        1071.5bp
        128.5M
        128.5M
        100.0%
        45.2M
        43.2M
        95.7%
        38.4M
        85.0%
        4.8M
        27.2%
        93.3%
        10947.6Mb
        90.3M
        51.8%
        98.7%
        1.9%
        ERR5974737_1
        64.5%
        51.0%
        131bp
        147bp
        18%
        45.8M
        64.7%
        51.0%
        130bp
        142bp
        18%
        45.2M
        ERR5974737_2
        62.5%
        51.0%
        131bp
        147bp
        18%
        45.8M
        63.1%
        51.0%
        130bp
        142bp
        18%
        45.2M
        ERR5974738
        0.0
        0.1
        46.8%
        1.15
        55.7M
        84.5M
        11.2M
        2.3M
        3.0M
        41.1%
        0.29%
        25.2M
        111.5M
        100.0%
        100.0%
        2.3%
        111.5M
        963.1bp
        136.6M
        136.6M
        100.0%
        57.9M
        55.7M
        96.2%
        51.5M
        89.0%
        4.2M
        30.2%
        93.6%
        13736.9Mb
        115.8M
        51.1%
        99.0%
        1.8%
        ERR5974738_1
        63.7%
        51.0%
        128bp
        137bp
        18%
        58.5M
        64.0%
        51.0%
        127bp
        132bp
        18%
        57.9M
        ERR5974738_2
        62.1%
        51.0%
        128bp
        137bp
        18%
        58.5M
        62.7%
        51.0%
        127bp
        132bp
        18%
        57.9M
        ERR5974739
        0.0
        0.1
        46.0%
        1.15
        58.0M
        83.6M
        14.4M
        2.7M
        3.6M
        40.6%
        0.35%
        29.5M
        116.0M
        100.0%
        100.0%
        2.5%
        116.0M
        1031.5bp
        145.4M
        145.4M
        100.0%
        61.0M
        58.0M
        95.1%
        52.8M
        86.7%
        5.1M
        28.1%
        93.2%
        14754.1Mb
        122.0M
        51.8%
        98.9%
        2.0%
        ERR5974739_1
        61.9%
        51.0%
        131bp
        142bp
        27%
        61.6M
        62.2%
        51.0%
        130bp
        137bp
        27%
        61.0M
        ERR5974739_2
        59.6%
        51.0%
        131bp
        142bp
        27%
        61.6M
        60.3%
        51.0%
        130bp
        137bp
        27%
        61.0M
        ERR5974740
        0.0
        0.2
        40.1%
        1.15
        48.2M
        71.5M
        11.7M
        2.5M
        3.1M
        47.7%
        0.33%
        18.2M
        96.4M
        100.0%
        100.0%
        1.8%
        96.4M
        1076.2bp
        114.6M
        114.6M
        100.0%
        50.4M
        48.2M
        95.6%
        44.8M
        89.0%
        3.4M
        23.0%
        93.2%
        12144.6Mb
        100.8M
        52.5%
        98.9%
        1.5%
        ERR5974740_1
        57.5%
        52.0%
        130bp
        142bp
        18%
        50.9M
        57.8%
        52.0%
        129bp
        142bp
        18%
        50.4M
        ERR5974740_2
        55.3%
        52.0%
        130bp
        142bp
        18%
        50.9M
        55.8%
        52.0%
        129bp
        142bp
        18%
        50.4M
        ERR5974741
        0.0
        0.5
        68.6%
        1.18
        59.9M
        94.9M
        6.4M
        2.5M
        3.5M
        23.9%
        0.32%
        28.3M
        119.9M
        100.0%
        100.0%
        2.1%
        119.9M
        1230.8bp
        148.1M
        148.1M
        100.0%
        62.9M
        59.9M
        95.3%
        54.7M
        86.9%
        5.3M
        43.3%
        93.4%
        15339.3Mb
        125.8M
        50.3%
        98.9%
        1.7%
        ERR5974741_1
        75.8%
        50.0%
        131bp
        150bp
        18%
        63.6M
        76.2%
        50.0%
        131bp
        147bp
        18%
        62.9M
        ERR5974741_2
        74.1%
        50.0%
        131bp
        150bp
        18%
        63.6M
        74.8%
        50.0%
        131bp
        147bp
        27%
        62.9M
        ERR5974742
        0.0
        0.2
        58.7%
        1.16
        58.3M
        90.7M
        7.6M
        2.2M
        3.1M
        31.1%
        0.34%
        28.9M
        116.5M
        100.0%
        100.0%
        2.2%
        116.5M
        1221.6bp
        145.5M
        145.5M
        100.0%
        61.5M
        58.3M
        94.7%
        52.7M
        85.6%
        5.6M
        36.2%
        92.9%
        15173.4Mb
        123.0M
        51.0%
        98.9%
        1.9%
        ERR5974742_1
        72.6%
        50.0%
        134bp
        150bp
        27%
        62.2M
        72.9%
        50.0%
        133bp
        150bp
        27%
        61.5M
        ERR5974742_2
        69.6%
        51.0%
        134bp
        150bp
        27%
        62.2M
        70.4%
        51.0%
        133bp
        150bp
        27%
        61.5M
        ERR5974743
        0.0
        0.4
        62.6%
        1.15
        36.8M
        58.8M
        3.3M
        1.4M
        2.3M
        26.7%
        0.34%
        21.9M
        73.6M
        100.0%
        100.0%
        3.3%
        73.6M
        1246.3bp
        95.6M
        95.6M
        100.0%
        38.5M
        36.8M
        95.7%
        33.4M
        86.9%
        3.4M
        37.7%
        93.0%
        9598.2Mb
        76.9M
        50.2%
        98.7%
        1.3%
        ERR5974743_1
        74.5%
        50.0%
        135bp
        150bp
        18%
        39.0M
        74.8%
        50.0%
        134bp
        150bp
        18%
        38.5M
        ERR5974743_2
        71.9%
        50.0%
        135bp
        150bp
        18%
        39.0M
        72.7%
        50.0%
        134bp
        150bp
        18%
        38.5M
        ERR5974744
        0.0
        0.3
        64.1%
        1.15
        39.5M
        62.8M
        3.1M
        1.3M
        2.6M
        26.9%
        0.32%
        19.6M
        78.9M
        100.0%
        100.0%
        2.3%
        78.9M
        1362.5bp
        98.5M
        98.5M
        100.0%
        41.0M
        39.5M
        96.2%
        35.8M
        87.2%
        3.7M
        40.3%
        93.3%
        10295.2Mb
        82.1M
        49.3%
        99.1%
        1.4%
        ERR5974744_1
        76.8%
        49.0%
        135bp
        150bp
        18%
        41.4M
        77.0%
        49.0%
        135bp
        150bp
        18%
        41.0M
        ERR5974744_2
        74.8%
        49.0%
        135bp
        150bp
        18%
        41.4M
        75.4%
        49.0%
        135bp
        150bp
        18%
        41.0M
        ERR5974745
        0.0
        0.4
        66.2%
        1.12
        48.5M
        78.6M
        3.6M
        1.8M
        2.8M
        25.6%
        0.33%
        23.1M
        97.1M
        100.0%
        100.0%
        2.1%
        97.1M
        1262.7bp
        120.2M
        120.2M
        100.0%
        50.7M
        48.5M
        95.8%
        44.2M
        87.2%
        4.4M
        41.6%
        93.5%
        12555.4Mb
        101.3M
        49.9%
        99.1%
        1.5%
        ERR5974745_1
        76.7%
        49.0%
        134bp
        150bp
        18%
        51.1M
        76.9%
        49.0%
        133bp
        150bp
        18%
        50.7M
        ERR5974745_2
        75.2%
        49.0%
        134bp
        150bp
        18%
        51.1M
        75.7%
        49.0%
        133bp
        150bp
        18%
        50.7M
        ERR5974746
        0.0
        0.2
        52.0%
        1.18
        61.2M
        96.0M
        8.8M
        2.7M
        3.5M
        37.9%
        0.34%
        24.4M
        122.5M
        100.0%
        100.0%
        1.8%
        122.5M
        1212.2bp
        146.9M
        146.9M
        100.0%
        63.8M
        61.2M
        95.9%
        56.5M
        88.6%
        4.7M
        30.3%
        92.6%
        15164.8Mb
        127.7M
        50.7%
        98.6%
        2.1%
        ERR5974746_1
        67.6%
        50.0%
        129bp
        142bp
        18%
        64.7M
        67.9%
        50.0%
        128bp
        137bp
        18%
        63.8M
        ERR5974746_2
        63.4%
        50.0%
        129bp
        142bp
        18%
        64.7M
        64.2%
        50.0%
        129bp
        137bp
        18%
        63.8M
        ERR5974747
        0.0
        0.9
        73.9%
        1.27
        43.6M
        69.3M
        6.8M
        1.3M
        2.4M
        21.5%
        0.34%
        12.7M
        87.2M
        100.0%
        100.0%
        1.3%
        87.2M
        1007.5bp
        99.9M
        99.9M
        100.0%
        44.8M
        43.6M
        97.3%
        41.1M
        91.8%
        2.5M
        45.6%
        93.7%
        10600.4Mb
        89.6M
        49.6%
        98.7%
        2.1%
        ERR5974747_1
        75.0%
        49.0%
        127bp
        137bp
        18%
        45.4M
        75.3%
        49.0%
        126bp
        137bp
        18%
        44.8M
        ERR5974747_2
        73.3%
        49.0%
        127bp
        137bp
        18%
        45.4M
        74.0%
        49.0%
        126bp
        137bp
        18%
        44.8M
        ERR5974748
        0.0
        0.9
        78.9%
        1.27
        58.2M
        92.2M
        6.5M
        2.1M
        3.8M
        15.5%
        0.33%
        29.3M
        116.4M
        100.0%
        100.0%
        2.7%
        116.4M
        1231.2bp
        145.7M
        145.7M
        100.0%
        60.4M
        58.2M
        96.3%
        53.4M
        88.4%
        4.8M
        49.5%
        92.5%
        14868.5Mb
        120.9M
        49.8%
        97.9%
        1.9%
        ERR5974748_1
        82.7%
        49.0%
        134bp
        150bp
        18%
        61.8M
        83.1%
        49.0%
        133bp
        150bp
        18%
        60.4M
        ERR5974748_2
        78.4%
        49.0%
        134bp
        150bp
        18%
        61.8M
        79.5%
        49.0%
        133bp
        150bp
        18%
        60.4M
        ERR5974749
        0.0
        0.5
        70.6%
        1.21
        57.9M
        93.7M
        4.1M
        1.7M
        2.9M
        20.7%
        0.31%
        36.9M
        115.8M
        100.0%
        100.0%
        3.5%
        115.8M
        1204.1bp
        152.7M
        152.7M
        100.0%
        60.5M
        57.9M
        95.7%
        52.3M
        86.4%
        5.6M
        46.0%
        93.7%
        14939.6Mb
        121.0M
        50.9%
        99.1%
        1.7%
        ERR5974749_1
        79.1%
        50.0%
        133bp
        150bp
        18%
        61.1M
        79.4%
        50.0%
        132bp
        147bp
        18%
        60.5M
        ERR5974749_2
        77.7%
        50.0%
        133bp
        150bp
        18%
        61.1M
        78.3%
        50.0%
        132bp
        147bp
        18%
        60.5M

        Sample status checks

        Reports on sample strandedness status, and any failures in trimming or mapping.

        Strandedness Checks

        The strandedness used for analysis in this workflow can either be provided by the user or automatically inferred by Salmon using a sample of reads. In both cases, strandedness is verified at the end of the workflow using RSeQC's infer_experiment.py on genomic alignments. In this table, a pass indicates a match between the supplied strandedness (or that inferred by Salmon) and RSeQC results. A fail indicates a mismatch or 'undetermined' strandedness. 'Undetermined' strandedness can signal QC issues, including potential genomic DNA contamination.

        Note: Rows are duplicated for an 'auto' setting to allow comparison of statistics between inference methods.

        Showing 82/82 rows and 7/7 columns.
        SampleStatusStrand inference methodProvided strandednessInferred strandednessSense (%)Antisense (%)Unstranded (%)
        ERR5974709
        pass
        RSeQC
        auto
        unstranded
        44.7
        44.5
        10.7
        ERR5974709
        pass
        Salmon
        auto
        unstranded
        49.7
        50.3
        0.0
        ERR5974710
        pass
        RSeQC
        auto
        unstranded
        44.1
        44.6
        11.3
        ERR5974710
        pass
        Salmon
        auto
        unstranded
        49.8
        50.2
        0.0
        ERR5974711
        pass
        RSeQC
        auto
        unstranded
        45.2
        45.1
        9.7
        ERR5974711
        pass
        Salmon
        auto
        unstranded
        49.7
        50.3
        0.0
        ERR5974712
        pass
        RSeQC
        auto
        unstranded
        42.4
        42.3
        15.3
        ERR5974712
        pass
        Salmon
        auto
        unstranded
        49.8
        50.2
        0.0
        ERR5974713
        pass
        RSeQC
        auto
        unstranded
        43.8
        43.7
        12.6
        ERR5974713
        pass
        Salmon
        auto
        unstranded
        49.8
        50.2
        0.0
        ERR5974714
        pass
        RSeQC
        auto
        unstranded
        42.8
        42.6
        14.6
        ERR5974714
        pass
        Salmon
        auto
        unstranded
        49.7
        50.3
        0.0
        ERR5974715
        pass
        RSeQC
        auto
        unstranded
        44.1
        44.3
        11.6
        ERR5974715
        pass
        Salmon
        auto
        unstranded
        49.8
        50.2
        0.0
        ERR5974716
        pass
        RSeQC
        auto
        unstranded
        44.5
        44.5
        11.0
        ERR5974716
        pass
        Salmon
        auto
        unstranded
        49.7
        50.3
        0.0
        ERR5974717
        pass
        RSeQC
        auto
        unstranded
        44.8
        44.6
        10.5
        ERR5974717
        pass
        Salmon
        auto
        unstranded
        49.6
        50.4
        0.0
        ERR5974718
        pass
        RSeQC
        auto
        unstranded
        45.5
        45.1
        9.4
        ERR5974718
        pass
        Salmon
        auto
        unstranded
        49.7
        50.3
        0.0
        ERR5974719
        pass
        RSeQC
        auto
        unstranded
        45.5
        45.2
        9.4
        ERR5974719
        pass
        Salmon
        auto
        unstranded
        49.7
        50.3
        0.0
        ERR5974720
        pass
        RSeQC
        auto
        unstranded
        45.1
        45.0
        9.9
        ERR5974720
        pass
        Salmon
        auto
        unstranded
        49.7
        50.3
        0.0
        ERR5974721
        pass
        RSeQC
        auto
        unstranded
        45.3
        45.8
        8.9
        ERR5974721
        pass
        Salmon
        auto
        unstranded
        49.7
        50.3
        0.0
        ERR5974722
        pass
        RSeQC
        auto
        unstranded
        44.5
        44.9
        10.6
        ERR5974722
        pass
        Salmon
        auto
        unstranded
        49.8
        50.2
        0.0
        ERR5974723
        pass
        RSeQC
        auto
        unstranded
        36.5
        36.7
        26.8
        ERR5974723
        pass
        Salmon
        auto
        unstranded
        49.8
        50.2
        0.0
        ERR5974724
        pass
        RSeQC
        auto
        unstranded
        44.8
        44.7
        10.5
        ERR5974724
        pass
        Salmon
        auto
        unstranded
        49.8
        50.2
        0.0
        ERR5974725
        pass
        RSeQC
        auto
        unstranded
        45.4
        44.9
        9.7
        ERR5974725
        pass
        Salmon
        auto
        unstranded
        49.7
        50.3
        0.0
        ERR5974726
        pass
        RSeQC
        auto
        unstranded
        36.2
        35.9
        27.9
        ERR5974726
        pass
        Salmon
        auto
        unstranded
        49.8
        50.2
        0.0
        ERR5974727
        pass
        RSeQC
        auto
        unstranded
        44.4
        44.2
        11.4
        ERR5974727
        pass
        Salmon
        auto
        unstranded
        49.7
        50.3
        0.0
        ERR5974728
        pass
        RSeQC
        auto
        unstranded
        44.9
        44.5
        10.6
        ERR5974728
        pass
        Salmon
        auto
        unstranded
        49.7
        50.3
        0.0
        ERR5974729
        pass
        RSeQC
        auto
        unstranded
        45.5
        45.3
        9.3
        ERR5974729
        pass
        Salmon
        auto
        unstranded
        49.7
        50.3
        0.0
        ERR5974730
        pass
        RSeQC
        auto
        unstranded
        45.4
        45.3
        9.3
        ERR5974730
        pass
        Salmon
        auto
        unstranded
        49.8
        50.2
        0.0
        ERR5974731
        pass
        RSeQC
        auto
        unstranded
        44.7
        44.8
        10.4
        ERR5974731
        pass
        Salmon
        auto
        unstranded
        49.7
        50.3
        0.0
        ERR5974732
        pass
        RSeQC
        auto
        unstranded
        44.5
        44.2
        11.3
        ERR5974732
        pass
        Salmon
        auto
        unstranded
        49.8
        50.2
        0.0
        ERR5974733
        pass
        RSeQC
        auto
        unstranded
        44.5
        44.2
        11.3
        ERR5974733
        pass
        Salmon
        auto
        unstranded
        49.7
        50.3
        0.0
        ERR5974734
        pass
        RSeQC
        auto
        unstranded
        45.2
        45.4
        9.4
        ERR5974734
        pass
        Salmon
        auto
        unstranded
        49.7
        50.3
        0.0
        ERR5974735
        pass
        RSeQC
        auto
        unstranded
        45.5
        45.4
        9.0
        ERR5974735
        pass
        Salmon
        auto
        unstranded
        49.8
        50.2
        0.0
        ERR5974736
        pass
        RSeQC
        auto
        unstranded
        44.7
        44.4
        11.0
        ERR5974736
        pass
        Salmon
        auto
        unstranded
        49.8
        50.2
        0.0
        ERR5974737
        pass
        RSeQC
        auto
        unstranded
        44.5
        45.1
        10.3
        ERR5974737
        pass
        Salmon
        auto
        unstranded
        49.9
        50.1
        0.0
        ERR5974738
        pass
        RSeQC
        auto
        unstranded
        45.3
        45.1
        9.6
        ERR5974738
        pass
        Salmon
        auto
        unstranded
        49.7
        50.3
        0.0
        ERR5974739
        pass
        RSeQC
        auto
        unstranded
        45.1
        45.2
        9.7
        ERR5974739
        pass
        Salmon
        auto
        unstranded
        49.7
        50.3
        0.0
        ERR5974740
        pass
        RSeQC
        auto
        unstranded
        45.7
        45.6
        8.7
        ERR5974740
        pass
        Salmon
        auto
        unstranded
        49.8
        50.2
        0.0
        ERR5974741
        pass
        RSeQC
        auto
        unstranded
        44.4
        44.9
        10.7
        ERR5974741
        pass
        Salmon
        auto
        unstranded
        49.7
        50.3
        0.0
        ERR5974742
        pass
        RSeQC
        auto
        unstranded
        42.7
        42.7
        14.6
        ERR5974742
        pass
        Salmon
        auto
        unstranded
        49.6
        50.4
        0.0
        ERR5974743
        pass
        RSeQC
        auto
        unstranded
        43.7
        43.8
        12.5
        ERR5974743
        pass
        Salmon
        auto
        unstranded
        49.7
        50.3
        0.0
        ERR5974744
        pass
        RSeQC
        auto
        unstranded
        44.4
        44.5
        11.1
        ERR5974744
        pass
        Salmon
        auto
        unstranded
        49.8
        50.2
        0.0
        ERR5974745
        pass
        RSeQC
        auto
        unstranded
        41.5
        41.8
        16.7
        ERR5974745
        pass
        Salmon
        auto
        unstranded
        49.6
        50.4
        0.0
        ERR5974746
        pass
        RSeQC
        auto
        unstranded
        43.5
        43.7
        12.9
        ERR5974746
        pass
        Salmon
        auto
        unstranded
        49.6
        50.4
        0.0
        ERR5974747
        pass
        RSeQC
        auto
        unstranded
        43.3
        43.3
        13.3
        ERR5974747
        pass
        Salmon
        auto
        unstranded
        50.0
        50.0
        0.0
        ERR5974748
        pass
        RSeQC
        auto
        unstranded
        43.1
        43.9
        13.1
        ERR5974748
        pass
        Salmon
        auto
        unstranded
        49.9
        50.1
        0.0
        ERR5974749
        pass
        RSeQC
        auto
        unstranded
        44.2
        44.1
        11.7
        ERR5974749
        pass
        Salmon
        auto
        unstranded
        49.7
        50.3
        0.0

        FastQC (raw)

        This section of the report shows FastQC results before adapter trimming.URL: http://www.bioinformatics.babraham.ac.uk/projects/fastqc

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Created with MultiQC

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Created with MultiQC

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Created with MultiQC

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Created with MultiQC

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Created with MultiQC

        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Created with MultiQC

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (e.g. PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Created with MultiQC

        Overrepresented sequences by sample

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Created with MultiQC

        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

        Showing 20/20 rows and 3/3 columns.
        Overrepresented sequenceReportsOccurrences% of all reads
        CTGGGATGCACCGGCCAGAGGCCATGCTGCTGCTGCTCACGCTTGCCCTC
        42
        3422852
        0.0744%
        CGAGAGCCCTGGGATGCACCGGCCAGAGGCCATGCTGCTGCTGCTCACGC
        15
        1121443
        0.0244%
        GTCACAGGCGAGAGCCCTGGGATGCACCGGCCAGAGGCCATGCTGCTGCT
        7
        522771
        0.0114%
        CAACCATTTACTTTTCCCTGAATGTTAGAAACTACAAAACCACTACCTTG
        3
        214528
        0.0047%
        GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
        2
        143387
        0.0031%
        GATCGGAAGAGCACACGTCTGAACTCCAGTCACC
        1
        137768
        0.0030%
        GTGATTTCATGGTCGTAGTCTTCAGTGGTGCTGAAATACTTGCCTCCTCC
        2
        136726
        0.0030%
        CTTCAGTGGTGCTGAAATACTTGCCTCCTCCAGGGCCATACATCTTCCCT
        2
        132491
        0.0029%
        GATCGGAAGAGCACACGTCTGAACTCCAGTCACCT
        1
        128547
        0.0028%
        TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
        2
        118396
        0.0026%
        CAGGAAGTCACCCTGCAGCCAGGCGAATACATCACAAAAGTCTTTGTCGC
        2
        115796
        0.0025%
        GCCACATTCAGTTCTTATCAAAGAAATAACCCAGACTTAATCTTGAATGA
        2
        106083
        0.0023%
        CCGTGATCCACAAGGCATTAGAGCATGGGTGGCATGGAGAAATCGTTGTC
        2
        96362
        0.0021%
        GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
        1
        95868
        0.0021%
        CGACAATCCAAAAACCTTCTACTGGGACTTTTACACCAACAGAACTGTGC
        2
        90417
        0.0020%
        GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
        1
        84838
        0.0018%
        CCCAGTTTCACGTCCCAGGAGTCTCCAAGTTTCACCTGGACACTTTTCAC
        1
        53098
        0.0012%
        GCTTAATATAAAATAACCACATTAGTGAACATTATATCTCTTAGAAGAAA
        1
        45488
        0.0010%
        GATCGGAAGAGCACACGTCTGAACTCCAGTCACCAA
        1
        45376
        0.0010%
        CTAAGATCTATTTAAGATAACCTTTTCTTATATTTTTTACTTAATATTGG
        1
        41929
        0.0009%

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Created with MultiQC

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        Created with MultiQC

        fastp

        All-in-one FASTQ preprocessor (QC, adapters, trimming, filtering, splitting...).URL: https://github.com/OpenGene/fastpDOI: 10.1093/bioinformatics/bty560

        Fastp goes through fastq files in a folder and perform a series of quality control and filtering. Quality control and reporting are displayed both before and after filtering, allowing for a clear depiction of the consequences of the filtering process. Notably, the latter can be conducted on a variety of parameters including quality scores, length, as well as the presence of adapters, polyG, or polyX tailing.

        Filtered Reads

        Filtering statistics of sampled reads.

        Created with MultiQC

        Insert Sizes

        Insert size estimation of sampled reads.

        Created with MultiQC

        Sequence Quality

        Average sequencing quality over each base of all reads.

        Created with MultiQC

        GC Content

        Average GC content over each base of all reads.

        Created with MultiQC

        N content

        Average N content over each base of all reads.

        Created with MultiQC


        FastQC (trimmed)

        This section of the report shows FastQC results after adapter trimming.URL: http://www.bioinformatics.babraham.ac.uk/projects/fastqc

        Sequence Counts

        Sequence counts for each sample. Duplicate read counts are an estimate only.

        This plot show the total number of reads, broken down into unique and duplicate if possible (only more recent versions of FastQC give duplicate info).

        You can read more about duplicate calculation in the FastQC documentation. A small part has been copied here for convenience:

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        Created with MultiQC

        Sequence Quality Histograms

        The mean quality value across each base position in the read.

        To enable multiple samples to be plotted on the same graph, only the mean quality scores are plotted (unlike the box plots seen in FastQC reports).

        Taken from the FastQC help:

        The y-axis on the graph shows the quality scores. The higher the score, the better the base call. The background of the graph divides the y axis into very good quality calls (green), calls of reasonable quality (orange), and calls of poor quality (red). The quality of calls on most platforms will degrade as the run progresses, so it is common to see base calls falling into the orange area towards the end of a read.

        Created with MultiQC

        Per Sequence Quality Scores

        The number of reads with average quality scores. Shows if a subset of reads has poor quality.

        From the FastQC help:

        The per sequence quality score report allows you to see if a subset of your sequences have universally low quality values. It is often the case that a subset of sequences will have universally poor quality, however these should represent only a small percentage of the total sequences.

        Created with MultiQC

        Per Base Sequence Content

        The proportion of each base position for which each of the four normal DNA bases has been called.

        To enable multiple samples to be shown in a single plot, the base composition data is shown as a heatmap. The colours represent the balance between the four bases: an even distribution should give an even muddy brown colour. Hover over the plot to see the percentage of the four bases under the cursor.

        To see the data as a line plot, as in the original FastQC graph, click on a sample track.

        From the FastQC help:

        Per Base Sequence Content plots out the proportion of each base position in a file for which each of the four normal DNA bases has been called.

        In a random library you would expect that there would be little to no difference between the different bases of a sequence run, so the lines in this plot should run parallel with each other. The relative amount of each base should reflect the overall amount of these bases in your genome, but in any case they should not be hugely imbalanced from each other.

        It's worth noting that some types of library will always produce biased sequence composition, normally at the start of the read. Libraries produced by priming using random hexamers (including nearly all RNA-Seq libraries) and those which were fragmented using transposases inherit an intrinsic bias in the positions at which reads start. This bias does not concern an absolute sequence, but instead provides enrichement of a number of different K-mers at the 5' end of the reads. Whilst this is a true technical bias, it isn't something which can be corrected by trimming and in most cases doesn't seem to adversely affect the downstream analysis.

        Click a sample row to see a line plot for that dataset.
        Rollover for sample name
        Position: -
        %T: -
        %C: -
        %A: -
        %G: -

        Per Sequence GC Content

        The average GC content of reads. Normal random library typically have a roughly normal distribution of GC content.

        From the FastQC help:

        This module measures the GC content across the whole length of each sequence in a file and compares it to a modelled normal distribution of GC content.

        In a normal random library you would expect to see a roughly normal distribution of GC content where the central peak corresponds to the overall GC content of the underlying genome. Since we don't know the GC content of the genome the modal GC content is calculated from the observed data and used to build a reference distribution.

        An unusually shaped distribution could indicate a contaminated library or some other kinds of biased subset. A normal distribution which is shifted indicates some systematic bias which is independent of base position. If there is a systematic bias which creates a shifted normal distribution then this won't be flagged as an error by the module since it doesn't know what your genome's GC content should be.

        Created with MultiQC

        Per Base N Content

        The percentage of base calls at each position for which an N was called.

        From the FastQC help:

        If a sequencer is unable to make a base call with sufficient confidence then it will normally substitute an N rather than a conventional base call. This graph shows the percentage of base calls at each position for which an N was called.

        It's not unusual to see a very low proportion of Ns appearing in a sequence, especially nearer the end of a sequence. However, if this proportion rises above a few percent it suggests that the analysis pipeline was unable to interpret the data well enough to make valid base calls.

        Created with MultiQC

        Sequence Length Distribution

        The distribution of fragment sizes (read lengths) found. See the FastQC help

        Created with MultiQC

        Sequence Duplication Levels

        The relative level of duplication found for every sequence.

        From the FastQC Help:

        In a diverse library most sequences will occur only once in the final set. A low level of duplication may indicate a very high level of coverage of the target sequence, but a high level of duplication is more likely to indicate some kind of enrichment bias (e.g. PCR over amplification). This graph shows the degree of duplication for every sequence in a library: the relative number of sequences with different degrees of duplication.

        Only sequences which first appear in the first 100,000 sequences in each file are analysed. This should be enough to get a good impression for the duplication levels in the whole file. Each sequence is tracked to the end of the file to give a representative count of the overall duplication level.

        The duplication detection requires an exact sequence match over the whole length of the sequence. Any reads over 75bp in length are truncated to 50bp for this analysis.

        In a properly diverse library most sequences should fall into the far left of the plot in both the red and blue lines. A general level of enrichment, indicating broad oversequencing in the library will tend to flatten the lines, lowering the low end and generally raising other categories. More specific enrichments of subsets, or the presence of low complexity contaminants will tend to produce spikes towards the right of the plot.

        Created with MultiQC

        Overrepresented sequences by sample

        The total amount of overrepresented sequences found in each library.

        FastQC calculates and lists overrepresented sequences in FastQ files. It would not be possible to show this for all samples in a MultiQC report, so instead this plot shows the number of sequences categorized as overrepresented.

        Sometimes, a single sequence may account for a large number of reads in a dataset. To show this, the bars are split into two: the first shows the overrepresented reads that come from the single most common sequence. The second shows the total count from all remaining overrepresented sequences.

        From the FastQC Help:

        A normal high-throughput library will contain a diverse set of sequences, with no individual sequence making up a tiny fraction of the whole. Finding that a single sequence is very overrepresented in the set either means that it is highly biologically significant, or indicates that the library is contaminated, or not as diverse as you expected.

        FastQC lists all the sequences which make up more than 0.1% of the total. To conserve memory only sequences which appear in the first 100,000 sequences are tracked to the end of the file. It is therefore possible that a sequence which is overrepresented but doesn't appear at the start of the file for some reason could be missed by this module.

        Created with MultiQC

        Top overrepresented sequences

        Top overrepresented sequences across all samples. The table shows 20 most overrepresented sequences across all samples, ranked by the number of samples they occur in.

        Showing 14/14 rows and 3/3 columns.
        Overrepresented sequenceReportsOccurrences% of all reads
        CTGGGATGCACCGGCCAGAGGCCATGCTGCTGCTGCTCACGCTTGCCCTC
        43
        3465354
        0.0761%
        CGAGAGCCCTGGGATGCACCGGCCAGAGGCCATGCTGCTGCTGCTCACGC
        15
        1118659
        0.0246%
        GTCACAGGCGAGAGCCCTGGGATGCACCGGCCAGAGGCCATGCTGCTGCT
        7
        521355
        0.0115%
        CAACCATTTACTTTTCCCTGAATGTTAGAAACTACAAAACCACTACCTTG
        3
        214186
        0.0047%
        GTGATTTCATGGTCGTAGTCTTCAGTGGTGCTGAAATACTTGCCTCCTCC
        3
        198513
        0.0044%
        CTTCAGTGGTGCTGAAATACTTGCCTCCTCCAGGGCCATACATCTTCCCT
        2
        132218
        0.0029%
        CAGGAAGTCACCCTGCAGCCAGGCGAATACATCACAAAAGTCTTTGTCGC
        2
        115536
        0.0025%
        GCCACATTCAGTTCTTATCAAAGAAATAACCCAGACTTAATCTTGAATGA
        2
        105868
        0.0023%
        CCCAGTTTCACGTCCCAGGAGTCTCCAAGTTTCACCTGGACACTTTTCAC
        2
        105326
        0.0023%
        CCGTGATCCACAAGGCATTAGAGCATGGGTGGCATGGAGAAATCGTTGTC
        2
        96211
        0.0021%
        CGACAATCCAAAAACCTTCTACTGGGACTTTTACACCAACAGAACTGTGC
        2
        90211
        0.0020%
        GCTTAATATAAAATAACCACATTAGTGAACATTATATCTCTTAGAAGAAA
        2
        86599
        0.0019%
        GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
        1
        62408
        0.0014%
        CTAAGATCTATTTAAGATAACCTTTTCTTATATTTTTTACTTAATATTGG
        1
        41861
        0.0009%

        Adapter Content

        The cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position.

        Note that only samples with ≥ 0.1% adapter contamination are shown.

        There may be several lines per sample, as one is shown for each adapter detected in the file.

        From the FastQC Help:

        The plot shows a cumulative percentage count of the proportion of your library which has seen each of the adapter sequences at each position. Once a sequence has been seen in a read it is counted as being present right through to the end of the read so the percentages you see will only increase as the read length goes on.

        Created with MultiQC

        Status Checks

        Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        FastQC assigns a status for each section of the report. These give a quick evaluation of whether the results of the analysis seem entirely normal (green), slightly abnormal (orange) or very unusual (red).

        It is important to stress that although the analysis results appear to give a pass/fail result, these evaluations must be taken in the context of what you expect from your library. A 'normal' sample as far as FastQC is concerned is random and diverse. Some experiments may be expected to produce libraries which are biased in particular ways. You should treat the summary evaluations therefore as pointers to where you should concentrate your attention and understand why your library may not look random and diverse.

        Specific guidance on how to interpret the output of each module can be found in the relevant report section, or in the FastQC help.

        In this heatmap, we summarise all of these into a single heatmap for a quick overview. Note that not all FastQC sections have plots in MultiQC reports, but all status checks are shown in this heatmap.

        Created with MultiQC

        DupRadar

        DupRadar provides duplication rate quality control for RNA-Seq datasets. Highly expressed genes can be expected to have a lot of duplicate reads, but high numbers of duplicates at low read counts can indicate low library complexity with technical duplication. This plot shows the general linear models - a summary of the gene duplication distributions.URL: bioconductor.org/packages/release/bioc/html/dupRadar.html

        Created with MultiQC

        Picard

        Tools for manipulating high-throughput sequencing data.URL: http://broadinstitute.github.io/picard

        Mark Duplicates

        Number of reads, categorised by duplication state. Pair counts are doubled - see help text for details.

        The table in the Picard metrics file contains some columns referring read pairs and some referring to single reads.

        To make the numbers in this plot sum correctly, values referring to pairs are doubled according to the scheme below:

        • READS_IN_DUPLICATE_PAIRS = 2 * READ_PAIR_DUPLICATES
        • READS_IN_UNIQUE_PAIRS = 2 * (READ_PAIRS_EXAMINED - READ_PAIR_DUPLICATES)
        • READS_IN_UNIQUE_UNPAIRED = UNPAIRED_READS_EXAMINED - UNPAIRED_READ_DUPLICATES
        • READS_IN_DUPLICATE_PAIRS_OPTICAL = 2 * READ_PAIR_OPTICAL_DUPLICATES
        • READS_IN_DUPLICATE_PAIRS_NONOPTICAL = READS_IN_DUPLICATE_PAIRS - READS_IN_DUPLICATE_PAIRS_OPTICAL
        • READS_IN_DUPLICATE_UNPAIRED = UNPAIRED_READ_DUPLICATES
        • READS_UNMAPPED = UNMAPPED_READS
        Created with MultiQC

        QualiMap

        Quality control of alignment data and its derivatives like feature counts.URL: http://qualimap.bioinfo.cipf.esDOI: 10.1093/bioinformatics/btv566; 10.1093/bioinformatics/bts503

        Genomic origin of reads

        Classification of mapped reads as originating in exonic, intronic or intergenic regions. These can be displayed as either the number or percentage of mapped reads.

        There are currently three main approaches to map reads to transcripts in an RNA-seq experiment: mapping reads to a reference genome to identify expressed transcripts that are annotated (and discover those that are unknown), mapping reads to a reference transcriptome, and de novo assembly of transcript sequences (Conesa et al. 2016).

        For RNA-seq QC analysis, QualiMap can be used to assess alignments produced by the first of these approaches. For input, it requires a GTF annotation file along with a reference genome, which can be used to reconstruct the exon structure of known transcripts. This allows mapped reads to be grouped by whether they originate in an exonic region (for QualiMap, this may include 5′ and 3′ UTR regions as well as protein-coding exons), an intron, or an intergenic region (see the Qualimap 2 documentation).

        The inferred genomic origins of RNA-seq reads are presented here as a bar graph showing either the number or percentage of mapped reads in each read dataset that have been assigned to each type of genomic region. This graph can be used to assess the proportion of useful reads in an RNA-seq experiment. That proportion can be reduced by the presence of intron sequences, especially if depletion of ribosomal RNA was used during sample preparation (Sims et al. 2014). It can also be reduced by off-target transcripts, which are detected in greater numbers at the sequencing depths needed to detect poorly-expressed transcripts (Tarazona et al. 2011).

        Created with MultiQC

        Gene Coverage Profile

        Mean distribution of coverage depth across the length of all mapped transcripts.

        There are currently three main approaches to map reads to transcripts in an RNA-seq experiment: mapping reads to a reference genome to identify expressed transcripts that are annotated (and discover those that are unknown), mapping reads to a reference transcriptome, and de novo assembly of transcript sequences (Conesa et al. 2016).

        For RNA-seq QC analysis, QualiMap can be used to assess alignments produced by the first of these approaches. For input, it requires a GTF annotation file along with a reference genome, which can be used to reconstruct the exon structure of known transcripts. QualiMap uses this information to calculate the depth of coverage along the length of each annotated transcript. For a set of reads mapped to a transcript, the depth of coverage at a given base position is the number of high-quality reads that map to the transcript at that position (Sims et al. 2014).

        QualiMap calculates coverage depth at every base position of each annotated transcript. To enable meaningful comparison between transcripts, base positions are rescaled to relative positions expressed as percentage distance along each transcript (0%, 1%, …, 99%). For the set of transcripts with at least one mapped read, QualiMap plots the cumulative mapped-read depth (y-axis) at each relative transcript position (x-axis). This plot shows the gene coverage profile across all mapped transcripts for each read dataset. It provides a visual way to assess positional biases, such as an accumulation of mapped reads at the 3′ end of transcripts, which may indicate poor RNA quality in the original sample (Conesa et al. 2016).

        The Normalised plot is calculated by MultiQC to enable comparison of samples with varying sequencing depth. The cumulative mapped-read depth at each position across the averaged transcript position are divided by the total for that sample across the entire averaged transcript.

        Created with MultiQC

        RSeQC

        Evaluates high throughput RNA-seq data.URL: http://rseqc.sourceforge.netDOI: 10.1093/bioinformatics/bts356

        Read Distribution

        Read Distribution calculates how mapped reads are distributed over genome features.

        Created with MultiQC

        Inner Distance

        Inner Distance calculates the inner distance (or insert size) between two paired RNA reads. Note that this can be negative if fragments overlap.

        Created with MultiQC

        Read Duplication

        read_duplication.py calculates how many alignment positions have a certain number of exact duplicates. Note - plot truncated at 500 occurrences and binned.

        Created with MultiQC

        Junction Annotation

        Junction annotation compares detected splice junctions to a reference gene model. An RNA read can be spliced 2 or more times, each time is called a splicing event.

        Created with MultiQC

        Junction Saturation

        Junction Saturation counts the number of known splicing junctions that are observed in each dataset. If sequencing depth is sufficient, all (annotated) splice junctions should be rediscovered, resulting in a curve that reaches a plateau. Missing low abundance splice junctions can affect downstream analysis.

        Created with MultiQC

        Infer experiment

        Infer experiment counts the percentage of reads and read pairs that match the strandedness of overlapping transcripts. It can be used to infer whether RNA-seq library preps are stranded (sense or antisense).

        Created with MultiQC

        Bam Stat

        All numbers reported in millions.

        Created with MultiQC

        Samtools

        Toolkit for interacting with BAM/CRAM files.URL: http://www.htslib.orgDOI: 10.1093/bioinformatics/btp352

        Percent mapped

        Alignment metrics from samtools stats; mapped vs. unmapped reads vs. reads mapped with MQ0.

        For a set of samples that have come from the same multiplexed library, similar numbers of reads for each sample are expected. Large differences in numbers might indicate issues during the library preparation process. Whilst large differences in read numbers may be controlled for in downstream processings (e.g. read count normalisation), you may wish to consider whether the read depths achieved have fallen below recommended levels depending on the applications.

        Low alignment rates could indicate contamination of samples (e.g. adapter sequences), low sequencing quality or other artefacts. These can be further investigated in the sequence level QC (e.g. from FastQC).

        Reads mapped with MQ0 often indicate that the reads are ambiguously mapped to multiple locations in the reference sequence. This can be due to repetitive regions in the genome, the presence of alternative contigs in the reference, or due to reads that are too short to be uniquely mapped. These reads are often filtered out in downstream analyses.

        Created with MultiQC

        Alignment stats

        This module parses the output from samtools stats. All numbers in millions.

        Created with MultiQC

        Flagstat

        This module parses the output from samtools flagstat

        Created with MultiQC

        Flagstat: Percentage of total

        This module parses the output from samtools flagstat

        Created with MultiQC

        XY counts

        Created with MultiQC

        Mapped reads per contig

        The samtools idxstats tool counts the number of mapped reads per chromosome / contig. Chromosomes with < 0.1% of the total aligned reads are omitted from this plot.

        Created with MultiQC

        STAR

        Universal RNA-seq aligner.URL: https://github.com/alexdobin/STARDOI: 10.1093/bioinformatics/bts635

        Summary Statistics

        Summary statistics from the STAR alignment

        Showing 41/41 rows and 10/19 columns.
        Sample NameTotal readsAlignedAlignedUniq alignedUniq alignedMultimappedAvg. read lenAvg. mapped lenSplicesAnnotated splicesGT/AG splicesGC/AG splicesAT/AC splicesNon-canonical splicesMismatch rateDel rateDel lenIns rateIns len
        ERR5974709
        64.0M
        61.2M
        95.6%
        56.6M
        88.4%
        4.6M
        263.0bp
        261.4bp
        48.0M
        47.9M
        47.5M
        0.4M
        0.0M
        0.1M
        0.3%
        0.0%
        1.8bp
        0.0%
        1.6bp
        ERR5974710
        45.6M
        43.4M
        95.0%
        39.8M
        87.1%
        3.6M
        260.0bp
        257.7bp
        31.5M
        31.5M
        31.1M
        0.3M
        0.0M
        0.1M
        0.3%
        0.0%
        1.8bp
        0.0%
        1.6bp
        ERR5974711
        62.4M
        59.4M
        95.2%
        54.2M
        86.9%
        5.2M
        258.0bp
        255.8bp
        46.7M
        46.6M
        46.2M
        0.3M
        0.0M
        0.1M
        0.3%
        0.0%
        2.1bp
        0.0%
        1.6bp
        ERR5974712
        59.7M
        57.0M
        95.4%
        52.9M
        88.5%
        4.1M
        250.0bp
        248.1bp
        43.1M
        43.0M
        42.6M
        0.4M
        0.0M
        0.1M
        0.3%
        0.0%
        1.8bp
        0.0%
        1.6bp
        ERR5974713
        45.5M
        43.7M
        96.1%
        40.7M
        89.6%
        2.9M
        264.0bp
        261.9bp
        33.0M
        32.9M
        32.6M
        0.3M
        0.0M
        0.0M
        0.3%
        0.0%
        1.8bp
        0.0%
        1.6bp
        ERR5974714
        42.0M
        40.3M
        96.0%
        37.6M
        89.5%
        2.7M
        259.0bp
        257.2bp
        28.7M
        28.6M
        28.4M
        0.2M
        0.0M
        0.0M
        0.3%
        0.0%
        1.8bp
        0.0%
        1.6bp
        ERR5974715
        61.3M
        58.4M
        95.3%
        53.3M
        86.9%
        5.2M
        262.0bp
        260.2bp
        48.1M
        48.0M
        47.5M
        0.4M
        0.0M
        0.1M
        0.4%
        0.0%
        1.9bp
        0.0%
        1.6bp
        ERR5974716
        50.1M
        47.8M
        95.4%
        44.3M
        88.5%
        3.5M
        254.0bp
        252.6bp
        37.5M
        37.5M
        37.1M
        0.3M
        0.0M
        0.1M
        0.3%
        0.0%
        2.1bp
        0.0%
        1.6bp
        ERR5974717
        45.8M
        43.8M
        95.7%
        40.3M
        88.0%
        3.5M
        254.0bp
        252.3bp
        34.8M
        34.8M
        34.4M
        0.3M
        0.0M
        0.0M
        0.3%
        0.0%
        1.8bp
        0.0%
        1.5bp
        ERR5974718
        52.4M
        50.3M
        96.1%
        46.1M
        88.0%
        4.2M
        260.0bp
        258.7bp
        42.5M
        42.5M
        42.0M
        0.5M
        0.0M
        0.1M
        0.3%
        0.0%
        2.1bp
        0.0%
        1.5bp
        ERR5974719
        59.7M
        57.3M
        95.9%
        53.0M
        88.8%
        4.2M
        260.0bp
        258.3bp
        46.8M
        46.7M
        46.3M
        0.4M
        0.0M
        0.1M
        0.3%
        0.0%
        1.9bp
        0.0%
        1.6bp
        ERR5974720
        59.7M
        56.8M
        95.1%
        52.6M
        88.0%
        4.2M
        262.0bp
        260.2bp
        45.6M
        45.5M
        45.0M
        0.4M
        0.0M
        0.1M
        0.3%
        0.0%
        2.0bp
        0.0%
        1.6bp
        ERR5974721
        61.6M
        58.6M
        95.2%
        53.8M
        87.3%
        4.8M
        248.0bp
        246.8bp
        45.9M
        45.8M
        45.4M
        0.4M
        0.1M
        0.1M
        0.3%
        0.0%
        2.1bp
        0.0%
        1.6bp
        ERR5974722
        62.7M
        59.5M
        94.8%
        54.6M
        87.0%
        4.9M
        259.0bp
        256.5bp
        47.0M
        46.9M
        46.5M
        0.4M
        0.0M
        0.1M
        0.3%
        0.0%
        1.8bp
        0.0%
        1.6bp
        ERR5974723
        60.6M
        57.7M
        95.2%
        53.4M
        88.0%
        4.4M
        250.0bp
        248.4bp
        44.4M
        44.3M
        43.9M
        0.3M
        0.0M
        0.1M
        0.3%
        0.0%
        2.1bp
        0.0%
        1.7bp
        ERR5974724
        61.4M
        58.7M
        95.6%
        53.2M
        86.6%
        5.5M
        258.0bp
        256.2bp
        43.5M
        43.4M
        43.0M
        0.3M
        0.0M
        0.1M
        0.3%
        0.0%
        1.8bp
        0.0%
        1.6bp
        ERR5974725
        61.2M
        58.9M
        96.1%
        54.5M
        89.0%
        4.3M
        256.0bp
        253.9bp
        46.8M
        46.7M
        46.4M
        0.4M
        0.0M
        0.1M
        0.3%
        0.0%
        2.1bp
        0.0%
        1.6bp
        ERR5974726
        48.0M
        46.5M
        96.7%
        43.5M
        90.5%
        3.0M
        258.0bp
        256.5bp
        35.7M
        35.6M
        35.3M
        0.3M
        0.0M
        0.0M
        0.3%
        0.0%
        2.0bp
        0.0%
        1.6bp
        ERR5974727
        61.7M
        59.1M
        95.8%
        55.1M
        89.3%
        4.0M
        260.0bp
        258.4bp
        49.0M
        48.9M
        48.5M
        0.4M
        0.0M
        0.1M
        0.3%
        0.0%
        1.9bp
        0.0%
        1.5bp
        ERR5974728
        41.9M
        40.3M
        96.3%
        37.6M
        89.8%
        2.7M
        257.0bp
        255.8bp
        32.2M
        32.2M
        31.9M
        0.2M
        0.0M
        0.1M
        0.3%
        0.0%
        1.8bp
        0.0%
        1.6bp
        ERR5974729
        60.2M
        57.4M
        95.3%
        51.9M
        86.1%
        5.6M
        262.0bp
        260.4bp
        46.6M
        46.5M
        46.1M
        0.3M
        0.0M
        0.1M
        0.3%
        0.0%
        1.7bp
        0.0%
        1.7bp
        ERR5974730
        59.7M
        57.0M
        95.5%
        52.3M
        87.5%
        4.8M
        260.0bp
        258.3bp
        43.4M
        43.4M
        43.1M
        0.3M
        0.0M
        0.1M
        0.3%
        0.0%
        1.8bp
        0.0%
        1.6bp
        ERR5974731
        47.5M
        45.7M
        96.2%
        42.1M
        88.6%
        3.6M
        256.0bp
        254.6bp
        35.7M
        35.6M
        35.4M
        0.2M
        0.0M
        0.0M
        0.3%
        0.0%
        1.8bp
        0.0%
        1.6bp
        ERR5974732
        66.3M
        62.9M
        95.0%
        57.7M
        87.1%
        5.2M
        264.0bp
        262.4bp
        48.2M
        48.1M
        47.7M
        0.4M
        0.0M
        0.1M
        0.3%
        0.0%
        1.7bp
        0.0%
        1.7bp
        ERR5974733
        62.2M
        59.7M
        96.0%
        54.7M
        88.0%
        5.0M
        260.0bp
        258.4bp
        47.5M
        47.4M
        47.1M
        0.3M
        0.0M
        0.1M
        0.3%
        0.0%
        2.2bp
        0.0%
        1.6bp
        ERR5974734
        48.3M
        46.2M
        95.7%
        42.5M
        87.8%
        3.8M
        259.0bp
        258.3bp
        36.0M
        36.0M
        35.7M
        0.3M
        0.0M
        0.1M
        0.3%
        0.0%
        1.8bp
        0.0%
        1.6bp
        ERR5974735
        59.6M
        56.8M
        95.3%
        52.0M
        87.2%
        4.8M
        258.0bp
        256.6bp
        45.1M
        45.0M
        44.7M
        0.3M
        0.0M
        0.1M
        0.3%
        0.0%
        1.8bp
        0.0%
        1.6bp
        ERR5974736
        66.3M
        63.9M
        96.4%
        59.6M
        90.0%
        4.3M
        255.0bp
        253.2bp
        48.5M
        48.4M
        48.0M
        0.4M
        0.0M
        0.1M
        0.3%
        0.0%
        1.8bp
        0.0%
        1.6bp
        ERR5974737
        45.2M
        43.2M
        95.7%
        38.4M
        85.0%
        4.8M
        259.0bp
        257.7bp
        35.1M
        35.1M
        34.8M
        0.3M
        0.0M
        0.0M
        0.3%
        0.0%
        2.0bp
        0.0%
        1.6bp
        ERR5974738
        57.9M
        55.7M
        96.2%
        51.5M
        89.0%
        4.2M
        253.0bp
        251.7bp
        42.7M
        42.6M
        42.3M
        0.3M
        0.0M
        0.1M
        0.3%
        0.0%
        1.8bp
        0.0%
        1.6bp
        ERR5974739
        61.0M
        58.0M
        95.1%
        52.8M
        86.7%
        5.1M
        259.0bp
        257.2bp
        43.6M
        43.5M
        43.1M
        0.4M
        0.0M
        0.1M
        0.3%
        0.0%
        1.8bp
        0.0%
        1.6bp
        ERR5974740
        50.4M
        48.2M
        95.6%
        44.8M
        89.0%
        3.4M
        258.0bp
        256.2bp
        37.2M
        37.2M
        36.7M
        0.4M
        0.0M
        0.1M
        0.3%
        0.0%
        2.0bp
        0.0%
        1.7bp
        ERR5974741
        62.9M
        59.9M
        95.3%
        54.7M
        86.9%
        5.3M
        260.0bp
        259.1bp
        51.9M
        51.8M
        51.4M
        0.3M
        0.0M
        0.1M
        0.3%
        0.0%
        1.8bp
        0.0%
        1.6bp
        ERR5974742
        61.5M
        58.3M
        94.7%
        52.7M
        85.6%
        5.6M
        265.0bp
        263.1bp
        51.3M
        51.3M
        50.9M
        0.3M
        0.0M
        0.1M
        0.3%
        0.0%
        1.7bp
        0.0%
        1.6bp
        ERR5974743
        38.5M
        36.8M
        95.7%
        33.4M
        86.9%
        3.4M
        268.0bp
        266.9bp
        33.2M
        33.2M
        32.9M
        0.2M
        0.0M
        0.1M
        0.3%
        0.0%
        1.7bp
        0.0%
        1.7bp
        ERR5974744
        41.0M
        39.5M
        96.2%
        35.8M
        87.2%
        3.7M
        268.0bp
        267.1bp
        37.5M
        37.4M
        37.1M
        0.2M
        0.0M
        0.1M
        0.3%
        0.0%
        2.5bp
        0.0%
        1.7bp
        ERR5974745
        50.7M
        48.5M
        95.8%
        44.2M
        87.2%
        4.4M
        265.0bp
        263.5bp
        43.1M
        43.0M
        42.7M
        0.3M
        0.0M
        0.1M
        0.3%
        0.0%
        1.9bp
        0.0%
        1.6bp
        ERR5974746
        63.8M
        61.2M
        95.9%
        56.5M
        88.6%
        4.7M
        256.0bp
        254.4bp
        53.0M
        53.0M
        52.5M
        0.4M
        0.0M
        0.1M
        0.3%
        0.0%
        2.0bp
        0.0%
        1.6bp
        ERR5974747
        44.8M
        43.6M
        97.3%
        41.1M
        91.8%
        2.5M
        252.0bp
        251.0bp
        36.6M
        36.5M
        36.3M
        0.2M
        0.0M
        0.0M
        0.3%
        0.0%
        1.9bp
        0.0%
        1.6bp
        ERR5974748
        60.4M
        58.2M
        96.3%
        53.4M
        88.4%
        4.8M
        266.0bp
        264.6bp
        62.0M
        62.0M
        61.6M
        0.4M
        0.0M
        0.1M
        0.3%
        0.0%
        1.7bp
        0.0%
        1.6bp
        ERR5974749
        60.5M
        57.9M
        95.7%
        52.3M
        86.4%
        5.6M
        263.0bp
        261.8bp
        54.4M
        54.3M
        53.9M
        0.3M
        0.0M
        0.1M
        0.3%
        0.0%
        2.0bp
        0.0%
        1.8bp

        Alignment Scores

        Created with MultiQC

        Sample relationships

        Plots interrogating sample relationships, based on final count matrices.

        STAR_SALMON DESeq2 sample similarity

        is generated from clustering by Euclidean distances between DESeq2 rlog values for each sample in the deseq2_qc.r script.

        Created with MultiQC

        STAR_SALMON DESeq2 PCA plot

        PCA plot between samples in the experiment. These values are calculated using DESeq2 in the deseq2_qc.r script.

        Created with MultiQC

        Biotype Counts

        Biotype Counts shows reads overlapping genomic features of different biotypes, counted by featureCounts.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        GroupSoftwareVersion
        BEDTOOLS_GENOMECOV_FWbedtools2.31.1
        CUSTOM_GETCHROMSIZESgetchromsizes1.21
        CUSTOM_TX2GENEpython3.10.4
        DESEQ2_QC_STAR_SALMONbioconductor-deseq21.28.0
        r-base4.0.3
        DupRadarbioconductor-dupradar1.32.0
        FASTQC_RAWfastqc0.12.1
        FASTQC_TRIMfastqc0.12.1
        FQ_LINTfq0.12.0 (2024-07-08)
        FQ_SUBSAMPLEfq0.12.0 (2024-07-08)
        GTF2BEDperl5.26.2
        GTF_FILTERpython3.9.5
        GUNZIP_FASTAgunzip1.13
        GUNZIP_GTFgunzip1.13
        MAKE_TRANSCRIPTS_FASTArsem1.3.1
        star2.7.10a
        MULTIQC_CUSTOM_BIOTYPEpython3.9.5
        PICARD_MARKDUPLICATESpicard3.1.1
        QUALIMAP_RNASEQqualimap2.3
        RSEQC_BAMSTATrseqc5.0.2
        RSEQC_INFEREXPERIMENTrseqc5.0.2
        RSEQC_INNERDISTANCErseqc5.0.2
        RSEQC_JUNCTIONANNOTATIONrseqc5.0.2
        RSEQC_JUNCTIONSATURATIONrseqc5.0.2
        RSEQC_READDISTRIBUTIONrseqc5.0.2
        RSEQC_READDUPLICATIONrseqc5.0.2
        SALMON_INDEXsalmon1.10.3
        SALMON_QUANTsalmon1.10.3
        SAMTOOLS_FLAGSTATsamtools1.21
        SAMTOOLS_IDXSTATSsamtools1.21
        SAMTOOLS_INDEXsamtools1.21
        SAMTOOLS_SORTsamtools1.21
        SAMTOOLS_STATSsamtools1.21
        SE_GENE_UNIFIEDbioconductor-summarizedexperiment1.32.0
        SE_TRANSCRIPT_UNIFIEDbioconductor-summarizedexperiment1.32.0
        STAR_ALIGNgawk5.1.0
        samtools1.21
        star2.7.11b
        STAR_GENOMEGENERATEgawk5.1.0
        samtools1.21
        star2.7.11b
        STRINGTIE_STRINGTIEstringtie2.2.3
        SUBREAD_FEATURECOUNTSsubread2.0.6
        TXIMETA_TXIMPORTbioconductor-tximeta1.20.1
        UCSC_BEDCLIPucsc377
        UCSC_BEDGRAPHTOBIGWIGucsc469
        WorkflowNextflow25.04.6
        nf-core/rnaseqv3.20.0-gb971ba1
        fastpfastp0.24.0

        nf-core/rnaseq Methods Description

        Suggested text and references to use when describing pipeline usage within the methods section of a publication.URL: https://github.com/nf-core/rnaseq

        Methods

        Data was processed using nf-core/rnaseq v3.20.0 (doi: 10.5281/zenodo.1400710) of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

        The pipeline was executed with Nextflow v25.04.6 (Di Tommaso et al., 2017) with the following command:

        nextflow run nf-core/rnaseq -r 3.20.0 -profile singularity -with-tower -resume --input ./samplesheet.csv --outdir ../results --gencode true --fasta ../../genomes/GRCh38.primary_assembly.genome.fa.gz --gtf ../../genomes/gencode.v43.annotation.gtf.gz --trimmer fastp --skip_pseudo_alignment --aligner star_salmon

        References

        • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
        • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
        • Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
        • da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
        Notes:
        • The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
        • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.

        nf-core/rnaseq Workflow Summary

        Input/output options

        input
        ./samplesheet.csv
        outdir
        ../results

        Reference genome options

        fasta
        ../../genomes/GRCh38.primary_assembly.genome.fa.gz
        gencode
        true
        gtf
        ../../genomes/gencode.v43.annotation.gtf.gz

        Read trimming options

        trimmer
        fastp

        Process skipping options

        skip_pseudo_alignment
        true

        Generic options

        trace_report_suffix
        2025-09-04_08-42-10

        Core Nextflow options

        configFiles
        /home/gmdazevedo/.nextflow/config, /home/gmdazevedo/.nextflow/assets/nf-core/rnaseq/nextflow.config
        containerEngine
        singularity
        launchDir
        /mnt/beegfs/scratch/gmdazevedo/rstudio/sjogren_rnaseq/ERP129369/assets
        profile
        singularity
        projectDir
        /home/gmdazevedo/.nextflow/assets/nf-core/rnaseq
        revision
        3.20.0
        runName
        marvelous_leibniz
        userName
        gmdazevedo
        workDir
        /mnt/beegfs/scratch/gmdazevedo/rstudio/sjogren_rnaseq/ERP129369/assets/work